One of my clients registered cash scheme VAT on 1st June.

in September their clients paid for the invoices issued in May ( before they are VAT registered). Shall I charge VAT on that?

Just thinking aloud - cash scheme charges on any income credit in your bank from 1st June. so these payment are subject to VAT.

however, if they registered  accrual VAT scheme, then they don't need to pay VAT.

I am confused, can anyone help me out? 

Many thanks
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Whilst waiting for the company to be VAT registered you cannot charge your clients for VAT.

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Therefore sales invoices issued before the EDR are excluded from the VAT return even for cash accounting schemes.
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